1MI7

Crystal Structure of Domain Swapped trp Aporepressor in 30%(v/v) Isopropanol

• PDB DOI: https://doi.org/10.2210/pdb1MI7/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-08-22 Released: 2003-09-02 
• Deposition Author(s): Lawson, C.L., Benoff, B., Berger, T., Berman, H.M., Carey, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.288 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6ST6

Literature

E. coli trp repressor forms a domain-swapped array in aqueous alcohol.

Lawson, C.L., Benoff, B., Berger, T., Berman, H.M., Carey, J.

(2004) Structure 12: 1099-1108

• PubMed: 15274929 
• DOI: https://doi.org/10.1016/j.str.2004.03.019
• Primary Citation of Related Structures:  
  1MI7


• PubMed Abstract: 
  

  The E. coli trp repressor (trpR) homodimer recognizes its palindromic DNA binding site through a pair of flexible helix-turn-helix (HTH) motifs displayed on an intertwined helical core. Flexible N-terminal arms mediate association between dimers bound to tandem DNA sites. The 2.5 A X-ray structure of trpR crystallized in 30% (v/v) isopropanol reveals a substantial conformational rearrangement of HTH motifs and N-terminal arms, with the protein appearing in the unusual form of an ordered 3D domain-swapped supramolecular array. Small angle X-ray scattering measurements show that the self-association properties of trpR in solution are fundamentally altered by isopropanol.

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Organizational Affiliation: 

Rutgers University, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, NJ 08854, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.3 kDa 
• Atom Count: 881 
• Modelled Residue Count: 103 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trp operon repressor	A [auth R]	107	Escherichia coli	Mutation(s): 0  Gene Names: trpR
UniProt
Find proteins for P0A881 (Escherichia coli (strain K12)) Explore P0A881  Go to UniProtKB:  P0A881

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	B [auth R]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.288 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.31	α = 90
b = 85.31	β = 90
c = 113.968	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-02 
Deposition Author(s): Lawson, C.L., Benoff, B., Berger, T., Berman, H.M., Carey, J.

Revision History  

• Version 1.0: 2003-09-02
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description